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1 <tool id="vcffilter2" name="VCFfilter:" version="0.0.2">
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2 <requirements>
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3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
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4 </requirements>
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5 <description>filter VCF data in a variety of attributes</description>
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6 <command>
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7 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
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8 ln -s "${input1}" input1.vcf.gz &&
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9 ln -s "${Tabixized_input}" input1.vcf.gz.tbi &&
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10 vcffilter ${filterList} input1.vcf.gz > "${out_file1}"
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11 </command>
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12
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13 <inputs>
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14 <param name="filterList" size="40" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below">
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15 <sanitizer>
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16 <valid initial="string.printable">
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17 <remove value="'"/>
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18 </valid>
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19 <mapping initial="none">
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20 <add source="'" target="__sq__"/>
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21 </mapping>
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22 </sanitizer>
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23 </param>
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24 <param format="vcf_bgzip" name="input1" type="data" label="VCF dataset to filter">
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25 <conversion name="Tabixized_input" type="tabix" />
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="vcf" name="out_file1" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="filterList" value="-f "DP > 10""/>
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34 <param name="input1" value="vcflib.vcf"/>
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35 <output name="out_file1" file="vcffilter-test1.vcf"/>
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36 </test>
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37 </tests>
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38 <help>
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39
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40 You can specify the following options within the **Specify filtering expression** box in any combination::
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41
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42 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
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43 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
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44 -s, --filter-sites filter entire records, not just alleles
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45 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
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46 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
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47 -A, --append-filter append the existing filter tag, don't just replace it
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48 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
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49 -v, --invert inverts the filter, e.g. grep -v
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50 -o, --or use logical OR instead of AND to combine filters
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51 -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g)
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52
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53 Filters are specified in the form {ID} {operator} {value}::
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54
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55 -f "DP > 10" # for info fields
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56 -g "GT = 1|1" # for genotype fields
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57 -f "CpG" # for 'flag' fields
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58
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59 Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.
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60
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61 Operators can be any of: =, !, <, >, pipe, &
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62
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63
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64 To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
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65
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66 -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20
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67 -r chrX # only output call on chromosome X
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68
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69 -----
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70
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71 Vcffilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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72
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73 </help>
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74 </tool>
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